Radix Cynanchi bungei (RCb) contains 40–70 % starch, yet little is known about the structure and properties of RCb starch. In this study, the multiscale structure of two cultivars of RCb starch (YW201501 and BW201001) were characterized, and the effects of starch structure on its physicochemical properties were investigated. The differences in physicochemical properties of RCb starch were influenced by its multiscale structure. The starch granules were round and irregular polygon, with sizes ranging between 2 and 14 μm. YW201501 had a higher amylose (21.81 %) and lipid (0.96 %) content, molecular weight (59.5 × 10⁶ g/mol), and A chain proportion (27.5 %), and a lower average granule size (6.14 μm), amylopectin average chain length (19.7), and B3 chain proportion (10.3 %). Both starches were B-type crystalline, with higher crystallinity (26.3 %) and R_1047/1022 (0.74) for YW201501, resulting in large gelatinization enthalpy. In addition, the higher peak viscosity and larger retrogradation degree of YW201501 were correlated to its higher amylose content. In vitro digestibility revealed that the low rapidly digestible starch and high resistant starch of BW201001 were related to the fine structure of starch. YW201501 and BW201001 had a medium glycemic index (62.6–66.0) with potential for processing into healthy starchy foods.